Clustering of scientific fields by integrating text mining and bibliometrics.

De toenemende verspreiding van wetenschappelijke en technologische publicaties via het internet, en de beschikbaarheid ervan in grootschalige bibliografische databanken, leiden tot enorme mogelijkheden om de wetenschap en technologie in kaart te brengen. Ook de voortdurende toename van beschikbare rekenkracht en de ontwikkeling van nieuwe algoritmen dragen hiertoe bij. Belangrijke uitdagingen blijven echter bestaan. Dit proefschrift bevestigt de hypothese dat de nauwkeurigheid van zowel het clusteren van wetenschappelijke kennisgebieden als het classificeren van publicaties nog verbeterd kunnen worden door het integreren van tekstontginning en bibliometrie. Zowel de tekstuele als de bibliometrische benadering hebben voor- en nadelen, en allebei bieden ze een andere kijk op een corpus van wetenschappelijke publicaties of patenten. Enerzijds is er een schat aan tekstinformatie aanwezig in dergelijke documenten, anderzijds vormen de onderlinge citaties grote netwerken die extra informatie leveren. We integreren beide gezichtspunten en tonen hoe bestaande tekstuele en bibliometrische methoden kunnen verbeterd worden. De dissertatie is opgebouwd uit drie delen: Ten eerste bespreken we het gebruik van tekstontginningstechnieken voor informatievergaring en voor het in kaart brengen van kennis vervat in teksten. We introduceren en demonstreren het raamwerk voor tekstontginning, evenals het gebruik van agglomeratieve hiërarchische clustering. Voorts onderzoeken we de relatie tussen enerzijds de performantie van het clusteren en anderzijds het gewenste aantal clusters en het aantal factoren bij latent semantische indexering. Daarnaast beschrijven we een samengestelde, semi-automatische strategie om het aantal clusters in een verzameling documenten te bepalen. Ten tweede behandelen we netwerken die bestaan uit citaties tussen wetenschappelijke documenten en netwerken die ontstaan uit onderlinge samenwerkingsverbanden tussen auteurs. Dergelijke netwerken kunnen geanalyseerd worden met technieken van de bibliometrie en de grafentheorie, met als doel het rangschikken van relevante entiteiten, het clusteren en het ontdekken van gemeenschappen. Ten derde tonen we de complementariteit aan van tekstontginning en bibliometrie en stellen we mogelijkheden voor om beide werelden op correcte wijze te integreren. De performantie van ongesuperviseerd clusteren en van classificeren verbetert significant door het samenvoegen van de tekstuele inhoud van wetenschappelijke publicaties en de structuur van citatienetwerken. Een methode gebaseerd op statistische meta-analyse behaalt de beste resultaten en overtreft methoden die enkel gebaseerd zijn op tekst of citaties. Onze geïntegreerde of hybride strategieën voor informatievergaring en clustering worden gedemonstreerd in twee domeinstudies. Het doel van de eerste studie is het ontrafelen en visualiseren van de conceptstructuur van de informatiewetenschappen en het toetsen van de toegevoegde waarde van de hybride methode. De tweede studie omvat de cognitieve structuur, bibliometrische eigenschappen en de dynamica van bio-informatica. We ontwikkelen een methode voor dynamisch en geïntegreerd clusteren van evoluerende bibliografische corpora. Deze methode vergelijkt en volgt clusters doorheen de tijd. Samengevat kunnen we stellen dat we voor de complementaire tekst- en netwerkwerelden een hybride clustermethode ontwerpen die tegelijkertijd rekening houdt met beide paradigma's. We tonen eveneens aan dat de geïntegreerde zienswijze een beter begrip oplevert van de structuur en de evolutie van wetenschappelijke kennisgebieden.SISTA;

Persistent Homology in Multivariate Data Visualization

Technological advances of recent years have changed the way research is done. When describing complex phenomena, it is now possible to measure and model a myriad of different aspects pertaining to them. This increasing number of variables, however, poses significant challenges for the visual analysis and interpretation of such multivariate data. Yet, the effective visualization of structures in multivariate data is of paramount importance for building models, forming hypotheses, and understanding intrinsic properties of the underlying phenomena. This thesis provides novel visualization techniques that advance the field of multivariate visual data analysis by helping represent and comprehend the structure of high-dimensional data. In contrast to approaches that focus on visualizing multivariate data directly or by means of their geometrical features, the methods developed in this thesis focus on their topological properties. More precisely, these methods provide structural descriptions that are driven by persistent homology, a technique from the emerging field of computational topology. Such descriptions are developed in two separate parts of this thesis. The first part deals with the qualitative visualization of topological features in multivariate data. It presents novel visualization methods that directly depict topological information, thus permitting the comparison of structural features in a qualitative manner. The techniques described in this part serve as low-dimensional representations that make the otherwise high-dimensional topological features accessible. We show how to integrate them into data analysis workflows based on clustering in order to obtain more information about the underlying data. The efficacy of such combined workflows is demonstrated by analysing complex multivariate data sets from cultural heritage and political science, for example, whose structures are hidden to common visualization techniques. The second part of this thesis is concerned with the quantitative visualization of topological features. It describes novel methods that measure different aspects of multivariate data in order to provide quantifiable information about them. Here, the topological characteristics serve as a feature descriptor. Using these descriptors, the visualization techniques in this part focus on augmenting and improving existing data analysis processes. Among others, they deal with the visualization of high-dimensional regression models, the visualization of errors in embeddings of multivariate data, as well as the assessment and visualization of the results of different clustering algorithms. All the methods presented in this thesis are evaluated and analysed on different data sets in order to show their robustness. This thesis demonstrates that the combination of geometrical and topological methods may support, complement, and surpass existing approaches for multivariate visual data analysis

Shape Retrieval Methods for Architectural 3D Models

This thesis introduces new methods for content-based retrieval of architecture-related 3D models. We thereby consider two different overall types of architectural 3D models. The first type consists of context objects that are used for detailed design and decoration of 3D building model drafts. This includes e.g. furnishing for interior design or barriers and fences for forming the exterior environment. The second type consists of actual building models. To enable efficient content-based retrieval for both model types that is tailored to the user requirements of the architectural domain, type-specific algorithms must be developed. On the one hand, context objects like furnishing that provide similar functions (e.g. seating furniture) often share a similar shape. Nevertheless they might be considered to belong to different object classes from an architectural point of view (e.g. armchair, elbow chair, swivel chair). The differentiation is due to small geometric details and is sometimes only obvious to an expert from the domain. Building models on the other hand are often distinguished according to the underlying floor- and room plans. Topological floor plan properties for example serve as a starting point for telling apart residential and commercial buildings. The first contribution of this thesis is a new meta descriptor for 3D retrieval that combines different types of local shape descriptors using a supervised learning approach. The approach enables the differentiation of object classes according to small geometric details and at the same time integrates expert knowledge from the field of architecture. We evaluate our approach using a database containing arbitrary 3D models as well as on one that only consists of models from the architectural domain. We then further extend our approach by adding a sophisticated shape descriptor localization strategy. Additionally, we exploit knowledge about the spatial relationship of object components to further enhance the retrieval performance. In the second part of the thesis we introduce attributed room connectivity graphs (RCGs) as a means to characterize a 3D building model according to the structure of its underlying floor plans. We first describe how RCGs are inferred from a given building model and discuss how substructures of this graph can be queried efficiently. We then introduce a new descriptor denoted as Bag-of-Attributed-Subgraphs that transforms attributed graphs into a vector-based representation using subgraph embeddings. We finally evaluate the retrieval performance of this new method on a database consisting of building models with different floor plan types. All methods presented in this thesis are aimed at an as automated as possible workflow for indexing and retrieval such that only minimum human interaction is required. Accordingly, only polygon soups are required as inputs which do not need to be manually repaired or structured. Human effort is only needed for offline groundtruth generation to enable supervised learning and for providing information about the orientation of building models and the unit of measurement used for modeling

Optimum Average Silhouette Width Clustering Methods

Cluster analysis is the search for groups of alike instances in the data. The two major problems in cluster analysis are: how many clusters are present in the data? And how can the actual clustering solution be found? We have developed a unified approach to estimate number of clusters and clustering solution mutually. This work is about theory, methodology and algorithm developed of newly proposed approach. // Average silhouette width (ASW) is a well-known index for measuring the clustering quality and for the estimation of the number of clusters. The index is in wide use across disciplines as standard practice for these tasks. In this work the clustering methodolo- gies is proposed that can itself estimate number of clusters on the fly, as well as produce the clustering against this estimated number by optimizing the ASW index. The performance of the ASW index for these two tasks are meticulously investigated. // ASW based clustering functions are proposed for the two most popular clustering domains i.e., hierarchical and non-hierarchical. The performance comparison for clustering solutions obtained from the proposed methods with a range of clustering methods has been done for the quality evaluation. // The performance comparison for the estimation of the number of clusters of the proposed methods has been made using a wide spectrum of cluster estimation indices and methods. For this, large scale studies for the estimation of the number of clusters have been conducted with well-reputed clustering methods to find out each method’s estimation performance with different indices/methods for various kinds of clustering structures. // Developing mathematical and theoretical aspects for clustering is a relatively new and challenging avenue. Recently this research domain has received considerable attention due to the present need and importance of theory of clustering. The purpose behind the theory development for clustering is to make the general nature of clustering more understandable without assuming particular data generating structures and independently from any clustering algorithm/functions. Lastly, a considerable amount of attention has been drawn towards the theory development of the ASW index in the latter part of the thesis

Computation in Complex Networks

Complex networks are one of the most challenging research focuses of disciplines, including physics, mathematics, biology, medicine, engineering, and computer science, among others. The interest in complex networks is increasingly growing, due to their ability to model several daily life systems, such as technology networks, the Internet, and communication, chemical, neural, social, political and financial networks. The Special Issue “Computation in Complex Networks" of Entropy offers a multidisciplinary view on how some complex systems behave, providing a collection of original and high-quality papers within the research fields of: • Community detection • Complex network modelling • Complex network analysis • Node classification • Information spreading and control • Network robustness • Social networks • Network medicin

Enhanced clustering analysis pipeline for performance analysis of parallel applications

Clustering analysis is widely used to stratify data in the same cluster when they are similar according to the specific metrics. We can use the cluster analysis to group the CPU burst of a parallel application, and the regions on each process in-between communication calls or calls to the parallel runtime. The resulting clusters obtained are the different computational trends or phases that appear in the application. These clusters are useful to understand the behavior of the computation part of the application and focus the analyses on those that present performance issues. Although density-based clustering algorithms are a powerful and efficient tool to summarize this type of information, their traditional user-guided clustering methodology has many shortcomings and deficiencies in dealing with the complexity of data, the diversity of data structures, high-dimensionality of data, and the dramatic increase in the amount of data. Consequently, the majority of DBSCAN-like algorithms have weaknesses to handle high-dimensionality and/or Multi-density data, and they are sensitive to their hyper-parameter configuration. Furthermore, extracting insight from the obtained clusters is an intuitive and manual task. To mitigate these weaknesses, we have proposed a new unified approach to replace the user-guided clustering with an automated clustering analysis pipeline, called Enhanced Cluster Identification and Interpretation (ECII) pipeline. To build the pipeline, we propose novel techniques including Robust Independent Feature Selection, Feature Space Curvature Map, Organization Component Analysis, and hyper-parameters tuning to feature selection, density homogenization, cluster interpretation, and model selection which are the main components of our machine learning pipeline. This thesis contributes four new techniques to the Machine Learning field with a particular use case in Performance Analytics field. The first contribution is a novel unsupervised approach for feature selection on noisy data, called Robust Independent Feature Selection (RIFS). Specifically, we choose a feature subset that contains most of the underlying information, using the same criteria as the Independent component analysis. Simultaneously, the noise is separated as an independent component. The second contribution of the thesis is a parametric multilinear transformation method to homogenize cluster densities while preserving the topological structure of the dataset, called Feature Space Curvature Map (FSCM). We present a new Gravitational Self-organizing Map to model the feature space curvature by plugging the concepts of gravity and fabric of space into the Self-organizing Map algorithm to mathematically describe the density structure of the data. To homogenize the cluster density, we introduce a novel mapping mechanism to project the data from the non-Euclidean curved space to a new Euclidean flat space. The third contribution is a novel topological-based method to study potentially complex high-dimensional categorized data by quantifying their shapes and extracting fine-grain insights from them to interpret the clustering result. We introduce our Organization Component Analysis (OCA) method for the automatic arbitrary cluster-shape study without an assumption about the data distribution. Finally, to tune the DBSCAN hyper-parameters, we propose a new tuning mechanism by combining techniques from machine learning and optimization domains, and we embed it in the ECII pipeline. Using this cluster analysis pipeline with the CPU burst data of a parallel application, we provide the developer/analyst with a high-quality SPMD computation structure detection with the added value that reflects the fine grain of the computation regions.El análisis de conglomerados se usa ampliamente para estratificar datos en el mismo conglomerado cuando son similares según las métricas específicas. Nosotros puede usar el análisis de clúster para agrupar la ráfaga de CPU de una aplicación paralela y las regiones en cada proceso intermedio llamadas de comunicación o llamadas al tiempo de ejecución paralelo. Los clusters resultantes obtenidos son las diferentes tendencias computacionales o fases que aparecen en la solicitud. Estos clusters son útiles para entender el comportamiento de la parte de computación del aplicación y centrar los análisis en aquellos que presenten problemas de rendimiento. Aunque los algoritmos de agrupamiento basados en la densidad son una herramienta poderosa y eficiente para resumir este tipo de información, su La metodología tradicional de agrupación en clústeres guiada por el usuario tiene muchas deficiencias y deficiencias al tratar con la complejidad de los datos, la diversidad de estructuras de datos, la alta dimensionalidad de los datos y el aumento dramático en la cantidad de datos. En consecuencia, el La mayoría de los algoritmos similares a DBSCAN tienen debilidades para manejar datos de alta dimensionalidad y/o densidad múltiple, y son sensibles a su configuración de hiperparámetros. Además, extraer información de los clústeres obtenidos es una forma intuitiva y tarea manual Para mitigar estas debilidades, hemos propuesto un nuevo enfoque unificado para reemplazar el agrupamiento guiado por el usuario con un canalización de análisis de agrupamiento automatizado, llamada canalización de identificación e interpretación de clúster mejorada (ECII). para construir el tubería, proponemos técnicas novedosas que incluyen la selección robusta de características independientes, el mapa de curvatura del espacio de características, Análisis de componentes de la organización y ajuste de hiperparámetros para la selección de características, homogeneización de densidad, agrupación interpretación y selección de modelos, que son los componentes principales de nuestra canalización de aprendizaje automático. Esta tesis aporta cuatro nuevas técnicas al campo de Machine Learning con un caso de uso particular en el campo de Performance Analytics. La primera contribución es un enfoque novedoso no supervisado para la selección de características en datos ruidosos, llamado Robust Independent Feature. Selección (RIFS).Específicamente, elegimos un subconjunto de funciones que contiene la mayor parte de la información subyacente, utilizando el mismo criterios como el análisis de componentes independientes. Simultáneamente, el ruido se separa como un componente independiente. La segunda contribución de la tesis es un método de transformación multilineal paramétrica para homogeneizar densidades de clústeres mientras preservando la estructura topológica del conjunto de datos, llamado Mapa de Curvatura del Espacio de Características (FSCM). Presentamos un nuevo Gravitacional Mapa autoorganizado para modelar la curvatura del espacio característico conectando los conceptos de gravedad y estructura del espacio en el Algoritmo de mapa autoorganizado para describir matemáticamente la estructura de densidad de los datos. Para homogeneizar la densidad del racimo, introducimos un mecanismo de mapeo novedoso para proyectar los datos del espacio curvo no euclidiano a un nuevo plano euclidiano espacio. La tercera contribución es un nuevo método basado en topología para estudiar datos categorizados de alta dimensión potencialmente complejos mediante cuantificando sus formas y extrayendo información detallada de ellas para interpretar el resultado de la agrupación. presentamos nuestro Método de análisis de componentes de organización (OCA) para el estudio automático de forma arbitraria de conglomerados sin una suposición sobre el distribución de datos.Postprint (published version